LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
variable        sname index h2bulk

units 		electron
newton		on
boundary	p p p

atom_style	electron

read_data  	data.${sname}
read_data  	data.h2bulk
Reading data file ...
  orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  13718 atoms
  read_data CPU = 0.048 seconds

pair_style      eff/cut 30.627847
pair_coeff	* *

neigh_modify	one 20000 page 200000

comm_modify	vel yes

compute		effTemp all temp/eff

thermo          100
thermo_style    custom step pe temp press vol
thermo_modify	temp effTemp

# structure minimization
dump            1 all xyz 1 ${sname}.min.xyz
dump            1 all xyz 1 h2bulk.min.xyz
min_style	cg
minimize 	0 1.0e-4 1 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 20000, page size: 200000
  master list distance cutoff = 32.627847
  ghost atom cutoff = 32.627847
  binsize = 16.313924, bins = 4 4 4
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair eff/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 87.11 | 93.61 | 100.1 Mbytes
   Step         PotEng          Temp          Press          Volume    
         0  -2871.4801      0              2.8596879e+10  229847.29    
         1  -2872.8077      0              2.8046824e+10  229847.29    
Loop time of 1.02378 on 4 procs for 1 steps with 13718 atoms

100.0% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = max iterations
  Energy initial, next-to-last, final = 
     -2871.48013813359  -2871.48013813359   -2872.8076730722
  Force two-norm initial, final = 5.4264823 5.0563616
  Force max component initial, final = 0.21424475 0.19518835
  Final line search alpha, max atom move = 0.046675588 0.0091105311
  Iterations, force evaluations = 1 1

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.7704     | 0.89228    | 1.0165     |  11.0 | 87.16
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0028288  | 0.12705    | 0.24891    |  29.2 | 12.41
Output  | 0.0037898  | 0.0038794  | 0.0039584  |   0.1 |  0.38
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.0005774  |            |       |  0.06

Nlocal:         3429.5 ave        3800 max        3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost:        65600.5 ave       67122 max       64060 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs:    1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1

Total # of neighbors = 59740807
Ave neighs/atom = 4354.9211
Neighbor list builds = 0
Dangerous builds = 0
undump		1

# create initial velocities according to temp, w/out e radial dof
velocity 	all create 20000.0 4928459 rot yes dist gaussian

# npt
fix		1 all npt/eff temp 20000.0 20000.0 1.0 iso 1e9 1e9 1.0
variable       density equal 11.2058851*mass(all)
thermo_style    custom step pe temp press vol v_density
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
thermo_modify	temp effTemp

dump		2 all xyz 10000 ${sname}.npt.xyz
dump		2 all xyz 10000 h2bulk.npt.xyz
compute         1 all property/atom spin eradius
dump		3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
dump		3 all custom 10000 h2bulk.npt.lammpstrj id type x y z c_1[1] c_1[2]

thermo          1
run		10
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 79.61 | 86.11 | 92.6 Mbytes
   Step         PotEng          Temp          Press          Volume       v_density   
         1  -2872.8077      40002.916      1.392533e+11   229847.29      154332.61    
         2  -2872.8075      40002.808      1.3925254e+11  229847.72      154332.61    
         3  -2872.8072      40002.493      1.3925022e+11  229849.01      154332.61    
         4  -2872.8068      40001.97       1.3924633e+11  229851.15      154332.61    
         5  -2872.8064      40001.241      1.3924088e+11  229854.15      154332.61    
         6  -2872.8058      40000.304      1.3923386e+11  229858.01      154332.61    
         7  -2872.8052      39999.161      1.3922528e+11  229862.72      154332.61    
         8  -2872.8045      39997.81       1.3921514e+11  229868.29      154332.61    
         9  -2872.8037      39996.253      1.3920343e+11  229874.72      154332.61    
        10  -2872.8028      39994.488      1.3919016e+11  229882.01      154332.61    
        11  -2872.8018      39992.517      1.3917533e+11  229890.15      154332.61    
Loop time of 10.5538 on 4 procs for 10 steps with 13718 atoms

Performance: 81.866 fs/day, 0.293 hours/fs, 0.948 timesteps/s, 12.998 katom-step/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 8.6596     | 9.2995     | 10.519     |  24.8 | 88.12
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.029706   | 1.2492     | 1.8893     |  67.7 | 11.84
Output  | 0.00056676 | 0.00059312 | 0.00063847 |   0.0 |  0.01
Modify  | 0.0017284  | 0.0019179  | 0.0020891  |   0.4 |  0.02
Other   |            | 0.002503   |            |       |  0.02

Nlocal:         3429.5 ave        3800 max        3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost:        65600.5 ave       67122 max       64060 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs:    1.49356e+07 ave 1.64691e+07 max 1.33702e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1

Total # of neighbors = 59742327
Ave neighs/atom = 4355.0319
Neighbor list builds = 0
Dangerous builds = 0

unfix		1
undump		2
undump		3
Total wall time: 0:00:14
